Question on EMBOSS libraries (fwd)

Bill Shui touro at
Fri Jul 6 00:12:04 UTC 2001

Hi Alan,
    Bill here, I thought I should clarify my question.

    Basically, I didn't want to use emboss to write XML reports, it should
    be handled by the database system.

    I'm writing a bioinformatics plugin to a semi-structured database system.

    The the query would not be like SQL, but of the same essence.

    I had a look at the code, but I thought it really depends on lot of acd
    files, so everytime you want to run a program, you'll have to initialise
    pretty much all of the acd settings and loading matrices, etc.

    what I want to do is that all these settings, ie. matrices and codon
    tables will be loaded into the database management system's main kernel
    at the system start up.

    such that when a user later issue a command to run a certain program,
    it need not to reinitialize all the settings. Since I"m really breaking
    up all the emboss code to suit my need, I really need to know which
    routines in the ajax library are essential for the core computation, eg.
    routines that do the actual sequence alignments.

hope this clarified my previous question.

thanks in advance.



On Thu, Jul 05, 2001 at 04:46:11PM +0800, Jingchu Luo wrote:
> This is the feedback I got from Alan Bleasby, the EMBOSS head.
> ---------- Forwarded message ----------
> Date: Thu, 5 Jul 2001 08:41:22 +0100 (BST)
> From: ableasby at
> To: luojc at
> Subject: Re: Question on EMBOSS libraries (fwd)
> Indeed. The question is so vague though I don't know precisely
> what he wants. If you read the minutes of the last EMBOSS
> meeting (:-) last Friday then you'll see I volunteered
> to have emboss write XML reports as an option.
> Cheers old chum
> Alan

<Reed> It is important to note that the primary reason the
       Roman Empire fail is that they had no concept of
       zero... thus they could not test the success or
       failure of their C programs.
Bill Shui           Email:	wshui at
				touro at
				bill.shui at
Bioinformatics Programmer

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